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- PDB-6kdn: HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dGTP terna... -

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Basic information

Entry
Database: PDB / ID: 6kdn
TitleHIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dGTP ternary complex
Components
  • DNA/RNA (38-MER)
  • HIV-1 RT p51 subunit
  • HIV-1 reverse transcriptase p66 subunit
KeywordsTRANSFERASE/DNA / Entecavir 5'-triphosphate / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / TRANSFERASE-DNA complex / REPLICATION
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Retrovirus capsid, C-terminal / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Pol protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Human immunodeficiency virus type 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsYasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19fk0310113 Japan
CitationJournal: Sci Rep / Year: 2020
Title: Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine.
Authors: Yasutake, Y. / Hattori, S.I. / Tamura, N. / Matsuda, K. / Kohgo, S. / Maeda, K. / Mitsuya, H.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 reverse transcriptase p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,76215
Polymers255,2396
Non-polymers1,5239
Water7,963442
1
A: HIV-1 reverse transcriptase p66 subunit
B: HIV-1 RT p51 subunit
E: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4278
Polymers127,6193
Non-polymers8085
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-51 kcal/mol
Surface area46260 Å2
MethodPISA
2
C: HIV-1 reverse transcriptase p66 subunit
D: HIV-1 RT p51 subunit
F: DNA/RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3357
Polymers127,6193
Non-polymers7164
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-50 kcal/mol
Surface area46570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.167, 284.167, 95.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HIV-1 reverse transcriptase p66 subunit


Mass: 64033.387 Da / Num. of mol.: 2 / Mutation: Y214F, F215Y, Q250M, C261S, C379S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: D3XFN5, UniProt: P12497*PLUS
#2: Protein HIV-1 RT p51 subunit / HIV-1 reverse transcriptase p51 subunit / p51 RT


Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C749S, C867S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497

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DNA chain , 1 types, 2 molecules EF

#3: DNA chain DNA/RNA (38-MER)


Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 451 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 130151 / % possible obs: 100 % / Redundancy: 5.2 % / Rrim(I) all: 0.069 / Net I/σ(I): 17.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6400 / Rrim(I) all: 0.888 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XN1

5xn1


Resolution: 2.303→48.603 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.67
RfactorNum. reflection% reflection
Rfree0.221 6460 5.08 %
Rwork0.1863 --
obs0.1881 127260 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.303→48.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15690 1495 94 442 17721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00517876
X-RAY DIFFRACTIONf_angle_d0.72224585
X-RAY DIFFRACTIONf_dihedral_angle_d22.8576821
X-RAY DIFFRACTIONf_chiral_restr0.2492665
X-RAY DIFFRACTIONf_plane_restr0.0052831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3029-2.32910.36191960.32184061X-RAY DIFFRACTION99
2.3291-2.35650.31522190.28744040X-RAY DIFFRACTION100
2.3565-2.38530.29042160.27594030X-RAY DIFFRACTION100
2.3853-2.41540.33371900.27974003X-RAY DIFFRACTION100
2.4154-2.44720.32362420.26854076X-RAY DIFFRACTION100
2.4472-2.48080.27872460.25413947X-RAY DIFFRACTION100
2.4808-2.51620.29172390.24214015X-RAY DIFFRACTION100
2.5162-2.55370.30591880.24184039X-RAY DIFFRACTION100
2.5537-2.59360.31232330.24143989X-RAY DIFFRACTION100
2.5936-2.63620.28771810.23884069X-RAY DIFFRACTION100
2.6362-2.68160.28122250.23444017X-RAY DIFFRACTION100
2.6816-2.73040.28281910.23854055X-RAY DIFFRACTION100
2.7304-2.78290.26242050.23934051X-RAY DIFFRACTION100
2.7829-2.83970.26722250.22154010X-RAY DIFFRACTION100
2.8397-2.90140.26542250.21593995X-RAY DIFFRACTION100
2.9014-2.96890.24942380.21134038X-RAY DIFFRACTION100
2.9689-3.04310.25432570.21033973X-RAY DIFFRACTION100
3.0431-3.12540.2541810.20064053X-RAY DIFFRACTION100
3.1254-3.21740.24142300.19174016X-RAY DIFFRACTION100
3.2174-3.32120.23342080.19414038X-RAY DIFFRACTION100
3.3212-3.43990.24012160.18693997X-RAY DIFFRACTION100
3.4399-3.57750.21332190.17974059X-RAY DIFFRACTION100
3.5775-3.74030.20762010.17524049X-RAY DIFFRACTION100
3.7403-3.93740.19262400.16273979X-RAY DIFFRACTION100
3.9374-4.1840.19222160.15154030X-RAY DIFFRACTION100
4.184-4.50680.17272060.14984047X-RAY DIFFRACTION100
4.5068-4.960.16392160.14364011X-RAY DIFFRACTION100
4.96-5.67670.16562100.15474038X-RAY DIFFRACTION100
5.6767-7.14850.20062070.17114037X-RAY DIFFRACTION100
7.1485-48.61410.17351940.15354038X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.31410.0816-0.59660.629-0.16782.3196-0.14160.0401-0.0165-0.03790.0327-0.09450.1832-0.02150.06370.2132-0.00820.03590.2902-0.06070.3066178.1721275.4909-146.0189
23.26170.73980.32061.11840.53761.7256-0.23250.50680.165-0.19820.06360.3744-0.1304-0.61450.18270.28270.0027-0.03970.628-0.04230.4166146.0212276.2906-155.0778
31.33980.07610.08753.73281.77334.4002-0.1797-0.1031-0.404-0.23250.03020.16470.3032-0.37480.12070.2619-0.05060.07580.3465-0.02920.3307174.6347264.3106-147.6383
41.36250.1225-0.1581.1925-0.481.0186-0.00640.17910.1657-0.15590.03890.107-0.0514-0.0813-0.03630.2527-0.01720.03280.33090.00170.2676211.0255281.6876-182.7135
50.6359-0.1982-0.07661.6536-0.66971.17150.04040.01040.0057-0.0668-0.0341-0.12050.03250.2872-0.00230.2308-0.01730.03920.3823-0.00310.2847238.5334262.5969-181.4085
63.10890.67370.47031.6186-0.40422.64680.20310.4666-0.3228-0.196-0.379-0.07260.55520.16290.18410.42320.02940.07740.3818-0.03050.2854207.3243273.5807-190.5654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 553)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 427)
3X-RAY DIFFRACTION3(chain 'E' and resid -1 through 33)
4X-RAY DIFFRACTION4(chain 'C' and resid 1 through 553)
5X-RAY DIFFRACTION5(chain 'D' and resid 5 through 427)
6X-RAY DIFFRACTION6(chain 'F' and resid -4 through 33)

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